Density function M06 method has been used to optimize the geometries of shikonin -thymine at 6-311++G** basis. Finally, fourteen stabilized complexes have been obtained. Theories of atoms in molecules (AIM) and natural bond orbital (NBO) have been utilized to investigate the hydrogen bonds involved in all the systems. The interaction energies of all the complexes were corrected by basis set superposition error (BSSE). By the analysis interaction energy, charge density and second-order interaction energies E(2) of the complexes, it is found that complex 2 is the most stable structure.